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  11 <td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Peptide</h2>
  12 <font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
  13 </TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
  14 Sun 18 Jan 2009</B></td></tr></TABLE>
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  16
  17 <h2>Contents</h2>
  18 <ul>
  19         <li><a href="#pdb2gmx">Generating a topology file</a>
  20         <li><a href="#solvate">Solvate the peptide</a>
  21         <li><a href="#indexfile">Generate an index file</a>
  22         <li><a href="#em">Energy minimization</a>
  23         <li><a href="#posres">Molecular dynamics with position restraints</a>
  24         <li><a href="#full">Unrestrained molecular dynamics</a>
  25         <li><a href="#analysis">Analysis of trajectory files</a>
  26 </ul>
  27
  28 <A NAME="spep"><H2>Ribonuclease S-peptide</A></H2>
  29
  30 <p>Ribonuclease A is a digestive enzyme, secreted by the pancreas. The enzyme
  31 can be cleaved by subtilisin at a single peptide bond to yield
  32 Ribonuclease-S, a catalytically active complex of an S-peptide moiety
  33 (residues 1-20) and an S-protein moiety (residues 21-124), bound together
  34 by multiple non-covalent links (<A HREF=#stryer88>Stryer, 1988</A>).
  35 <P>
  36 The S-Peptide has been studied in many ways, experimentally
  37 as well as theoretically (simulation) because of the high a-helix
  38 content in solution, which is remarkable in such a small peptide.
  39 <P>
  40 All the files of speptide are stored in the directory <TT>
  41 tutor/speptide</TT>. First go to this directory:cd speptide
  42 <P>
  43 To be able to simulate the S-Peptide we need a starting structure. This can
  44 be taken from the protein data bank. There are a number of different
  45 structure for Ribonuclease S, from one of which we have cut out the
  46 first 20 residues, and stored it in
  47 <TT><a href="pdb.html">speptide.pdb</a></TT>.
  48 Have a look at the file
  49 <br><br>
  50 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  51 <tr NOSAVE>
  52 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  53 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  54
  55 <tt> more speptide.pdb
  56 </tt>
  57 <td></td>
  58 </tr>
  59 </table>
  60 <br>
  61 <p>
  62 If you have access to a molecular
  63 graphics program such as rasmol,
  64 you can look at the molecule on screen, eg:
  65 <br><br>
  66 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
  67 <tr NOSAVE>
  68 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
  69 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
  70
  71 <tt> rasmol speptide.pdb
  72 </tt>
  73 <td></td>
  74 </tr>
  75 </table>
  76 <br>
  77 <p>
  78
  79 The following steps have to be taken to perform a simulation of the peptide.
  80 <ol>
  81 <li>    Convert the pdb-file <a href="pdb.html">speptide.pdb</a>
  82         to a GROMACS structure file and a GROMACS topology file.
  83 <li>    Solvate the peptide in water
  84 <li>    Perform an energy minimization of the peptide in solvent
  85 <li>    Add ions if necessary (we will omit this step here)
  86 <li>    Perform a short MD run with position restraints on the peptide
  87 <li>    Perform full MD without restraints
  88 <li>    Analysis
  89 </ol><p>
  90
  91 We will describe in detail how such a simulation can be done,
  92 starting from a pdb-file.
  93
  94 <P><H3><A NAME="pdb2gmx">
  95 Generate a topology file (<tt><a href="top.html">.top</a></tt>) from the pdb-file (<tt><a href="pdb.html">.pdb</a></TT>)</a>
  96 </H3>
  97 <P>
  98 Generate a molecular topology and a structure file in
  99 format. This can be done with the <a href="pdb2gmx.html">pdb2gmx</a> program:
 100 <br><br>
 101 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 102 <tr NOSAVE>
 103 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 104 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 105
 106 <tt> pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro
 107 </tt>
 108 <td></td>
 109 </tr>
 110 </table>
 111 <br><p>
 112 Note that the correct file extension are added automatically to the
 113 filenames on the command line.
 114 You will only be asked to choose a forcefield, choose 0, but you can also
 115 have <a href="pdb2gmx.html">pdb2gmx</a> ask you
 116 about protonation of residues, and about protonation of N- and C-terminus.
 117 You can type
 118 <br><br>
 119 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 120 <tr NOSAVE>
 121 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 122 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 123
 124 <tt> pdb2gmx -h
 125 </tt>
 126 <td></td>
 127 </tr>
 128 </table>
 129 <br><p>
 130 to see the available options.
 131 <P>
 132 The <a href="pdb2gmx.html">
 133 pdb2gmx</a> program has generated a topology file
 134 <TT><a href="top.html">speptide.top</a></TT> and a
 135 GROMACS structure file <tt><a href="gro.html">speptide.gro</a></tt> and it will
 136 generate hydrogen
 137 positions. The <tt>-p</tt> and <tt>-o</tt> options with he
 138 filenames are optional; without them the files <TT><a href="top.html">topol.top</a></TT> and <TT>
 139 <a href="gro.html">conf.gro</a></TT> will be generated.
 140 Now have a look at the output from <a href="pdb2gmx.html">pdb2gmx</a>,
 141 <br><br>
 142 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 143 <tr NOSAVE>
 144 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 145 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 146
 147 <tt> more speptide.gro
 148 </tt>
 149 <td></td>
 150 </tr>
 151 </table>
 152 <br><p>
 153 You will see a close resemblance to the <a href="pdb.html">pdb</a> file, only the layout of
 154 the file is a bit different.
 155 Also do have a look at the topology
 156 <br><br>
 157 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 158 <tr NOSAVE>
 159 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 160 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 161
 162 <tt> more speptide.top
 163 </tt>
 164 <td></td>
 165 </tr>
 166 </table>
 167 <br><p>
 168 You will see a large file containing the atom types, the physical
 169 bonds between atoms, etcetera.
 170
 171 <P><H3><A NAME="solvate">
 172 Solvate the peptide in a periodic box filled with water</A></H3><p>
 173 This is done using the programs
 174 <a href="editconf.html">editconf</a> and
 175 <a href="genbox.html">genbox</a>.
 176 <a href="editconf.html">editconf</a>
 177 will make a rectangular box with empty space of user specified size
 178 around the molecule.
 179 <a href="genbox.html">genbox</a>
 180 will read the structure file and fill the box with water.
 181 <br><br>
 182 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 183 <tr NOSAVE>
 184 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 185 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 186
 187 <tt> editconf -f speptide -o -d 0.5<BR>
 188 genbox -cp out -cs -p speptide -o b4em
 189 </tt>
 190 <td></td>
 191 </tr>
 192 </table>
 193 <br><p>
 194 The program prints some lines of user information, like the volume of
 195 the box and the number of water molecules added to your
 196 peptide. <TT><a href="genbox.html">genbox</a></TT>
 197 also changes the topology file
 198 <TT><a href="top.html">speptide.top</a></TT> to include
 199 these water molecules in the topology. This can been seen by looking
 200 at the bottom of the
 201 <TT><a href="top.html">speptide.top</a></TT> file
 202 <br><br>
 203 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 204 <tr NOSAVE>
 205 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 206 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 207
 208 <tt> tail speptide.top
 209 </tt>
 210 <td></td>
 211 </tr>
 212 </table>
 213 <br><p>
 214 You will see some lines like
 215 <PRE>
 216 [ system ]
 217 ; Name          Number
 218 Protein         1
 219 SOL             N
 220 </PRE><p>
 221 where <tt>N</tt> is the number of water molecules added to your system by
 222 <TT><a href="genbox.html">genbox</a></TT>.
 223 <P>
 224
 225 It is also possible to solvate a peptide in another solvent such as
 226 dimethylsulfoxide (DMSO), as has been done by
 227 <A HREF=#mierke91>Mierke & Kessler, 1991</A>.
 228
 229 <P><H3><A NAME="indexfile">Generate index file (<TT><a href="ndx.html">.ndx</a></TT> extension)</A></H3>
 230 <p>
 231 By default, most GROMACS programs generate a set of index groups to select
 232 the most common subsets of atoms from your system (e.g. Protein, Backbone,
 233 C-alpha's, Solute, etc.).
 234 For the special cases when you need to select other groups than the
 235 default ones, an <a href="ndx.html">index file</a>
 236 can be generated using <a href="make_ndx.html">make_ndx</a>.
 237 This is an interactive program that lets you manipulate molecules,
 238 residues and atom. It's use should be self-explanatory.  To invoke the
 239 program you would
 240 <br><br>
 241 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 242 <tr NOSAVE>
 243 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 244 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 245
 246 <tt> make_ndx -f b4em
 247 </tt>
 248 <td></td>
 249 </tr>
 250 </table>
 251 <br><p>
 252 but don't bother for now.
 253
 254 <P><H3><A NAME="em">Perform an energy minimization of the peptide in solvent</A></H3>
 255 <p>
 256 Now we have to perform an <EM>energy minimization</EM> of the
 257 structure to remove the local strain in the peptide (due to generation
 258 of hydrogen positions) and to remove bad Van der Waals contacts
 259 (particles that are too close). This can be done with the
 260 <TT><a href="mdrun.html">mdrun</a></TT> program which
 261 is the MD and EM program. Before we can use the
 262 <TT> <a href="mdrun.html">mdrun</a></TT> program
 263 however, we have to preprocess the topology file (
 264 <TT><a href="top.html">speptide.top</a></TT>), the
 265 structure file (
 266 <TT><a href="gro.html">speptide.gro</a></TT>) and a
 267 special parameter file (<TT><a href="mdp_opt.html">em.mdp</a></TT>). Check
 268 the contents of this file
 269 <br><br>
 270 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 271 <tr NOSAVE>
 272 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 273 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 274
 275 <tt> more em.mdp
 276 </tt>
 277 <td></td>
 278 </tr>
 279 </table>
 280 <br><p>
 281 Preprocessing is done with the preprocessor called
 282 <TT><a href="grompp.html">grompp</a></TT>. This reads
 283 up the files just mentioned:
 284
 285 <br><br>
 286 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 287 <tr NOSAVE>
 288 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 289 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 290
 291 <tt> grompp -v -f em -c b4em -o em -p speptide
 292 </tt>
 293 <td></td>
 294 </tr>
 295 </table>
 296 <br><p>
 297 In this command the <tt>-v</tt> option turns on verbose mode, which
 298 gives a little bit of clarifying info on what the program is doing.
 299 We now have made a <EM>run input file</EM> (<TT><a href="tpr.html">em.tpr</a></TT>) which
 300 serves as input for the
 301 <TT><a href="mdrun.html">mdrun</a></TT> program. Now
 302 we can do the energy minimization:
 303 <br><br>
 304 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 305 <tr NOSAVE>
 306 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 307 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 308
 309 <tt> mdrun -v -s em -o em -c after_em -g emlog
 310 </tt>
 311 <td></td>
 312 </tr>
 313 </table>
 314 <br><p>
 315 In this command the <tt>-v</tt> option turns on verbose mode again.
 316 The <tt>-o</tt> option sets the filename for the trajectory file,
 317 which is not very important in energy minimizations. The <tt>-c</tt>
 318 option sets the filename of the structure file after energy
 319 minimization. This file we will subsequently use as input for the MD
 320 run.  The energy minimization takes some time, the amount depending on
 321 the CPU in your computer, the load of your computer, etc. The
 322 <TT><a href="mdrun.html">mdrun</a></TT> program is
 323 automatically <EM>niced</EM>; it runs at low priority. All programs
 324 that do extensive computations are automatically run at low
 325 priority. For most modern workstations this computation should be a
 326 matter of minutes. The minimization is finished when either the
 327 minimization has converged or a fixed number of steps has been
 328 performed.  Since the system consists merely of water, a quick check
 329 on the potential energy should reveal whether the minimization was
 330 successful: the potential energy of 1 SPC water molecule at 300 K is
 331 <tt>-42</tt> kJ mole<sup>-1</sup>. Since we have about <tt>2.55e+03</tt>
 332 SPC molecules the potential energy should be about <tt>-1.1e+5</tt> kJ
 333 mol<sup>-1</sup>. If the potential energy after minimization is lower
 334 than <tt>-1.1e+05</tt> kJ mol<sup>-1</sup> it is acceptable and the
 335 structure can be used for MD calculations.  After our EM calculation
 336 the program prints something like:
 337 <PRE>
 338 STEEPEST DESCENTS converged to 2000
 339   Potential Energy  = -1.19482e+05
 340 </PRE><p>
 341 which means our criterium is met, and we can proceed to the next step.
 342
 343 <P><H3><A NAME="posres">
 344 Perform a short MD run with position restraints on the peptide</A>
 345 </H3><p>
 346 Position restrained MD means Molecular Dynamics in which a part of the
 347 system is not allowed to move far off their starting positions.  To be
 348 able to run with position restraints we must add a section to the
 349 <TT><a href="top.html">speptide.top</a></TT> file,
 350 describing which atoms are to be restrained. Such a section is
 351 actually generated by the
 352 <a href="pdb2gmx.html">pdb2gmx</a> program. In the
 353 topology file it looks like
 354 <PRE>
 355 #ifdef POSRES<BR>
 356 #include "posres.itp"<BR>
 357 #endif
 358 </PRE><p>
 359 In the <a href="top.html">topology file</a> we use
 360 conditional inclusion, i.e. only if a variable <TT>POSRES</TT> is set
 361 in the preprocessor do we include the file, this allows us to use the
 362 same topology file for runs with and without position restraints. In
 363 the <a href="mdp_opt.html"><TT>pr.mdp</TT></a> parameter file
 364 for the position restraints this variable is set indeed:
 365 <PRE>
 366 define              =  -DPOSRES
 367 </PRE>
 368 <P>
 369 At last we can generate the input for the position restrained mdrun:
 370 <br><br>
 371 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 372 <tr NOSAVE>
 373 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 374 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 375
 376 <tt> grompp -f pr -o pr -c after_em -r after_em -p speptide
 377 </tt>
 378 <td></td>
 379 </tr>
 380 </table>
 381 <br><p>
 382 Now it's <a href="mdrun.html">MDrun</a> time:
 383 <br><br>
 384 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 385 <tr NOSAVE>
 386 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 387 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 388
 389 <tt> mdrun -v -s pr -e pr -o pr -c after_pr -g prlog >& pr.job &
 390 </tt>
 391 <td></td>
 392 </tr>
 393 </table>
 394 <br><p>
 395 This run is started in the background (it will take a while), you
 396 can watch how long it will take by typing:
 397 <br><br>
 398 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 399 <tr NOSAVE>
 400 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 401 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 402
 403 <tt> tail -f pr.job
 404 </tt>
 405 <td></td>
 406 </tr>
 407 </table>
 408 <br><p>
 409 With the <tt>Ctrl-C</tt> key you can kill the <tt>tail</tt> command.
 410 A good check of your simulation is to see whether density and potential
 411 energies have converged:
 412 <br><br>
 413 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 414 <tr NOSAVE>
 415 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 416 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 417
 418 <tt> g_energy -f pr -o out -w
 419 </tt>
 420 <td></td>
 421 </tr>
 422 </table>
 423 <br><p>
 424 The <a href="g_energy.html">
 425 g_energy</a> program will prompt you to select a number of energy terms
 426 from a list. For potential energy type:
 427 <br><br>
 428 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 429 <tr NOSAVE>
 430 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 431 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 432
 433 <tt> 9 0
 434 </tt>
 435 <td></td>
 436 </tr>
 437 </table>
 438 <br><p>
 439 If you have the xmgr program installed it will automatically pop up on your
 440 screen with the energy plot. You can do the same for the density
 441 and other energy terms, such as Solvent-Protein interactions.
 442
 443 <P><H3><A NAME="full">Perform full MD without restraints</A></H3>
 444 <p>Full MD is very similar to the restrained MD as far as GROMACS is
 445 concerned. Check out the <TT><a href="mdp_opt.html">full.mdp</a></TT> for details.
 446 <br><br>
 447 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 448 <tr NOSAVE>
 449 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 450 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 451
 452 <tt> grompp -v -f full -o full -c after_pr -p speptide
 453 </tt>
 454 <td></td>
 455 </tr>
 456 </table>
 457 <br><p>
 458 Then we can start mdrunning
 459 <br><br>
 460 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 461 <tr NOSAVE>
 462 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 463 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 464 <tt> mdrun -v -s full -e full -o full -c after_full -g flog >& full.job &
 465 </tt>
 466 <td></td>
 467 </tr>
 468 </table>
 469 <br><p>
 470 You should do similar convergence checks (and more!) as for the position
 471 restrained simulation.
 472
 473 <br><hr><br>
 474
 475 <P><H3><A NAME="analysis">Analysis</A></H3>
 476 <p>
 477 We will not describe analysis in detail, because most analysis tools
 478 are described in the Analysis chapter of the printed manual.
 479 We just list a few of the possibilities within GROMACS. By now you should be
 480 able to start programs yourself.
 481 <P>
 482 <oL>
 483 <LI><p> View the trajectory on your own X-screen (program
 484 <a href="ngmx.html">ngmx</a>).
 485 <br><br>
 486 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 487 <tr NOSAVE>
 488 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 489 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 490
 491 <tt> ngmx -s pr -f full
 492 </tt>
 493 <td></td>
 494 </tr>
 495 </table>
 496 <br>
 497 <font color="red">What happens to the peptide?</font>
 498 </p>
 499 </li>
 500
 501 <li><p>The Root Mean Square Deviation (RMSD) with respect to the crystal
 502 structure (program
 503 <a href="g_rms.html">g_rms</a>) is a measure of how well the
 504 crystal (starting) structure is maintained in the simulation.
 505 The RMSD at time t  is computed as
 506 &lt;(<b>r</b>(t)-<b>r</b>(0))<sup>2</sup>&gt;<sup>1/2</sup>
 507 after performing a least squares super position of the structure at
 508 time t onto the structure at time 0.
 509 <br><br>
 510 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 511 <tr NOSAVE>
 512 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 513 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 514
 515 <tt> g_rms -s pr -f full -o rmsd
 516 </tt>
 517 <td></td>
 518 </tr>
 519 </table>
 520 <br>
 521 Select the 1 for the number of groups, and select Calpha (Ca) for fitting
 522 and for computing the RMSD. View the output graph with xmgrace.
 523 <br><br>
 524 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 525 <tr NOSAVE>
 526 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 527 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 528
 529 <tt> xmgrace rmsd.xvg
 530 </tt>
 531 <td></td>
 532 </tr>
 533 </table>
 534 <br>
 535 <font color="red">Does the RMSD
 536 converge within the simulation? If not, what does this indicate?</font>
 537 </p>
 538
 539 <LI><p>The Radius of Gyration (Rg, program
 540 <a href="g_gyrate.html">g_gyrate</a>)) is a measure of the size of the
 541 protein. It is computed as the mean square distance of atoms from the center
 542 of mass of the molecule: Rg(t) = SUM<sub>i=1 .. N</sub>
 543 (<b>r</b><sub>i</sub>-<b>r</b><sub>com</sub>)<sup>2</sup>
 544 <br><br>
 545 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 546 <tr NOSAVE>
 547 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 548 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 549
 550 <tt> g_gyrate -s pr -f full -o gyrate
 551 </tt>
 552 <td></td>
 553 </tr>
 554 </table>
 555 <br>
 556 View the graph with xmgrace:
 557 <br><br>
 558 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 559 <tr NOSAVE>
 560 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 561 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 562
 563 <tt> xmgrace gyrate.xvg
 564 </tt>
 565 <td></td>
 566 </tr>
 567 </table>
 568 <br>
 569 <font color="red">Does the radius of gyration change during the
 570 simulation?</font>
 571 </P>
 572
 573 <LI><p>The Ramachandran Plot shows whether the backbone torsion angles
 574 (&phi;/&psi;) of your
 575 peptide are within the allowed region.
 576 (program <a href="g_rama.html">g_rama</a>).
 577 <br><br>
 578 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 579 <tr NOSAVE>
 580 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 581 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 582
 583 <tt> g_rama -s pr -f full -o rama
 584 </tt>
 585 <td></td>
 586 </tr>
 587 </table>
 588 <br>
 589 View the graph with xmgrace:
 590 <br><br>
 591 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 592 <tr NOSAVE>
 593 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 594 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 595
 596 <tt> xmgrace rama.xvg
 597 </tt>
 598 <td></td>
 599 </tr>
 600 </table>
 601 <br>
 602 Here you have all the backbone torsion angles from the trajectory.
 603 <font color="red">Are all the angles in the allowed region?
 604 What kind of structure do the angles indicate?</font>
 605 </P>
 606
 607 <LI><p>A salt bridge analysis (program
 608 <a href="g_saltbr.html">g_saltbr</a>) will tell you whether
 609 there are any saltbridges formed or broken during the simulation.
 610 It will also tell you about repulsive electrostatic interactions.
 611 <br><br>
 612 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 613 <tr NOSAVE>
 614 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 615 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 616
 617 <tt> g_saltbr -s pr -f full  -t 0.5 -sep
 618 </tt>
 619 <td></td>
 620 </tr>
 621 </table>
 622 <br>
 623 This will generate four graphs (in xmgrace format). Two of them refer to
 624 attractive interactions.
 625 You can view the graphs with xmgrace:
 626 <br><br>
 627 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 628 <tr NOSAVE>
 629 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 630 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 631 <tt>xmgrace sb-GLU2:ARG10.xvg sb-GLU2:LYSH7.xvg -legend load
 632 </tt>
 633 <td></td>
 634 </tr>
 635 </table>
 636 <br>
 637 <font color="red">Which interaction is the strongest?</font>
 638 Look at the peptide molecule again (using rasmol).
 639 <font color="red">Which atoms form the closest contact in the saltbridge?
 640 </font>
 641 </P>
 642
 643
 644 <LI> Secondary Structure analysis (program
 645 <a href="my_dssp.html">my_dssp</a>).
 646 This analysis uses the dssp (dictionary of secondary structure in proteins,
 647 <A HREF=#kabsch83>Kabsch & Sander, 1983</A>)  software.
 648 <br><br>
 649 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 650 <tr NOSAVE>
 651 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 652 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 653
 654 <tt> my_dssp -s pr -f full
 655 </tt>
 656 <td></td>
 657 </tr>
 658 </table>
 659 <br>
 660 Select protein when asked to select a group.
 661 You can postprecess the output file with:
 662 <br><br>
 663 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 664 <tr NOSAVE>
 665 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 666 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 667
 668 <tt> xpm2ps -f ss.xpm -o ss.eps
 669 </tt>
 670 <td></td>
 671 </tr>
 672 </table>
 673 <br>
 674 This will give you a postscript file which you can either print or
 675 view with xpsview.
 676 <br><br>
 677 <table BORDER=0 CELLSPACING=0 CELLPADDING=8 COLS=3 WIDTH="100%" NOSAVE >
 678 <tr NOSAVE>
 679 <td WIDTH="2%" NOSAVE><font color="#000000"></font></td>
 680 <td WIDTH="80%" BGCOLOR="#000066" NOSAVE><font color="#FFFFFF">
 681
 682 <tt> xpsview ss.eps
 683 </tt>
 684 <td></td>
 685 </tr>
 686 </table>
 687 <br>
 688 <font color="red">What happens to the Alpha helix (in blue)?</font>
 689
 690 </p>
 691 </li>
 692 </ol>
 693 <br><hr><br>
 694 <P>
 695 You have been witness of a full MD simulation starting from a pdb-file.
 696 It's that easy, but then again, maybe it was not that easy. The
 697 example presented here is a <EM>real</EM> example, this is how a
 698 production run should be performed, the complexity is in the process
 699 itself and not in the software (at least, that's our opinion).</p>
 700
 701 <hr>
 702 <a href="protunf.html"><h3>Go to the next step</h3></a>
 703 <hr>
 704
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